Rasayan
(the Sanskrit word for Chemistry) is a molecular modeling toolkit currently
under development. It permits the visualization of molecules and their
structure, and the computation of topological and geometric information
aimed to an efficient solution of the docking problem. Its user interface,
shown below, is based on X11 and Motif. Visualization is based on Open
Inventor and OpenGL.
It also allows to perform exact computation of Molecular Surfaces like the Solvent Accessible, the Solvent Contact and the Solvent Excluded surface (also known as the Connolly Surface) with NURBS patches so that they constitute both a exact boundary representation of the surface and allows direct display with standard graphics libraries like OpenGL.
The Rasayan toolkit is based on computation of the regular triangulation, power diagram and alpha-shape of a set of weighted points. Points in this application are centers of atoms, and weights are the square of their Van der Waals radii. Examples of weighted alpha-shapes (for increasing values of the parameter alpha) for the Nutrasweet molecule are shown below. Weighted alpha-shapes are described in
H. Edelsbrunner.Preliminary results on the use of alpha-shapes form molecular docking and similarity can be found in
``Weighted Alpha-Shapes''.
Tech Report UIUCDCS-R-92-1760, Dept. of Computer Science, University of Illinois at Urbana-Champaign, July 1992.
C. Bajaj, F. Bernardini, K. Sugihara.Alpha shape is also used as the basic geometric data structure for exact Molecular Surfaces computation:
``A Geometric Approach to Molecular Docking and Similarity''.
Computer Science Tech. Rep., CSD-TR-94-017, Purdue University, Mar. 1994.
C. Bajaj, H.Y. Lee, R. Merkert, V. PascucciBelow you can some Molecular Surface:
``NURBS based B-rep Models from Macromolecules and their Properties'',
In Proceedings Fourth Symposium on Solid Modeling and Applications, Atlanta,Georgia, 1997,C. Hoffmann and W. Bronsvort Eds., ACM Press. pp. 217-228
